process {
    withName: "DEEPVARIANT_MAKEEXAMPLES" {
        ext.args = '--checkpoint "/opt/models/wgs" --call_small_model_examples --small_model_indel_gq_threshold "30" --small_model_snp_gq_threshold "25" --small_model_vaf_context_window_size "51" --trained_small_model_path "/opt/smallmodels/wgs"'
    }
    withName: "DEEPVARIANT_CALLVARIANTS" {
        ext.args = '--checkpoint "/opt/models/wgs"'
    }

    // This configures RUNDEEPVARIANT, which is used as a reference for the correct test output
    withName: DEEPVARIANT_RUNDEEPVARIANT {
         ext.args = '--model_type=WGS '
         ext.prefix = { "${meta.id}_out" }
     }
}
